Computational study of the structure and electronic circular dichroism spectroscopy of blue copper proteins

The calculation of the electronic circular dichroism (CD) spectra of the oxidised form of the blue copper proteins plastocyanin and cucumber basic protein and the relationship between the observed spectral features and the structure of the active site of the protein is investigated. Excitation energ...

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Main Authors:	Do, Hainam, Deeth, Robert J., Besley, Nicholas A.
Format:	Article
Language:	English
Published:	American Chemical Society 2013
Online Access:	http://eprints.nottingham.ac.uk/29971/ http://eprints.nottingham.ac.uk/29971/ http://eprints.nottingham.ac.uk/29971/ http://eprints.nottingham.ac.uk/29971/1/blue-cd.pdf

id	nottingham-29971
recordtype	eprints
spelling	nottingham-299712017-10-12T19:36:06Z http://eprints.nottingham.ac.uk/29971/ Computational study of the structure and electronic circular dichroism spectroscopy of blue copper proteins Do, Hainam Deeth, Robert J. Besley, Nicholas A. The calculation of the electronic circular dichroism (CD) spectra of the oxidised form of the blue copper proteins plastocyanin and cucumber basic protein and the relationship between the observed spectral features and the structure of the active site of the protein is investigated. Excitation energies and transition strengths are computed using multi reference configuration interaction, and it is shown that computed spectra based on coordinates from the crystal structure or a single structure optimised in quantum mechanics/molecular mechanics (QM/MM) or ligand field molecular mechanics (LFMM) are qualitatively incorrect. In particular, the rotational strength of the ligand to metal charge transfer band is predicted to be too small or have the incorrect sign. By considering calculations on active site models with modified structures it is shown that the intensity of this band is sensitive to the non-planarity of the histidine and cysteine ligands coordinated to copper. Calculation of the ultraviolet absorption and CD spectra based upon averaging over many structures drawn from a LFMM molecular dynamics simulation are in good agreement with experiment, and superior to analogous calculations based upon structures from a classical molecular dynamics simulation. This provides evidence that the LFMM force field provides an accurate description of the molecular dynamics of these proteins. American Chemical Society 2013-06-17 Article PeerReviewed application/pdf en http://eprints.nottingham.ac.uk/29971/1/blue-cd.pdf Do, Hainam and Deeth, Robert J. and Besley, Nicholas A. (2013) Computational study of the structure and electronic circular dichroism spectroscopy of blue copper proteins. Journal of Physical Chemistry B, 117 (27). pp. 8105-8112. ISSN 1520-52707 http://pubs.acs.org/doi/abs/10.1021/jp404107j doi:10.1021/jp404107j doi:10.1021/jp404107j
repository_type	Digital Repository
institution_category	Local University
institution	University of Nottingham Malaysia Campus
building	Nottingham Research Data Repository
collection	Online Access
language	English
description	The calculation of the electronic circular dichroism (CD) spectra of the oxidised form of the blue copper proteins plastocyanin and cucumber basic protein and the relationship between the observed spectral features and the structure of the active site of the protein is investigated. Excitation energies and transition strengths are computed using multi reference configuration interaction, and it is shown that computed spectra based on coordinates from the crystal structure or a single structure optimised in quantum mechanics/molecular mechanics (QM/MM) or ligand field molecular mechanics (LFMM) are qualitatively incorrect. In particular, the rotational strength of the ligand to metal charge transfer band is predicted to be too small or have the incorrect sign. By considering calculations on active site models with modified structures it is shown that the intensity of this band is sensitive to the non-planarity of the histidine and cysteine ligands coordinated to copper. Calculation of the ultraviolet absorption and CD spectra based upon averaging over many structures drawn from a LFMM molecular dynamics simulation are in good agreement with experiment, and superior to analogous calculations based upon structures from a classical molecular dynamics simulation. This provides evidence that the LFMM force field provides an accurate description of the molecular dynamics of these proteins.
format	Article
author	Do, Hainam Deeth, Robert J. Besley, Nicholas A.
spellingShingle	Do, Hainam Deeth, Robert J. Besley, Nicholas A. Computational study of the structure and electronic circular dichroism spectroscopy of blue copper proteins
author_facet	Do, Hainam Deeth, Robert J. Besley, Nicholas A.
author_sort	Do, Hainam
title	Computational study of the structure and electronic circular dichroism spectroscopy of blue copper proteins
title_short	Computational study of the structure and electronic circular dichroism spectroscopy of blue copper proteins
title_full	Computational study of the structure and electronic circular dichroism spectroscopy of blue copper proteins
title_fullStr	Computational study of the structure and electronic circular dichroism spectroscopy of blue copper proteins
title_full_unstemmed	Computational study of the structure and electronic circular dichroism spectroscopy of blue copper proteins
title_sort	computational study of the structure and electronic circular dichroism spectroscopy of blue copper proteins
publisher	American Chemical Society
publishDate	2013
url	http://eprints.nottingham.ac.uk/29971/ http://eprints.nottingham.ac.uk/29971/ http://eprints.nottingham.ac.uk/29971/ http://eprints.nottingham.ac.uk/29971/1/blue-cd.pdf
first_indexed	2018-09-06T11:59:12Z
last_indexed	2018-09-06T11:59:12Z
_version_	1610859310995210240

Computational study of the structure and electronic circular dichroism spectroscopy of blue copper proteins

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